Package ubic.gemma.persistence.service.analysis.expression.diff

Interface DifferentialExpressionAnalysisService

All Superinterfaces:

AnalysisService<DifferentialExpressionAnalysis>

All Known Implementing Classes:

DifferentialExpressionAnalysisServiceImpl

public interface DifferentialExpressionAnalysisService
extends AnalysisService<DifferentialExpressionAnalysis>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Integer	countDownregulated(ExpressionAnalysisResultSet par, double threshold)
Integer	countProbesMeetingThreshold(ExpressionAnalysisResultSet ears, double threshold)
Integer	countUpregulated(ExpressionAnalysisResultSet par, double threshold)
DifferentialExpressionAnalysis	create(DifferentialExpressionAnalysis analysis)
Collection<DifferentialExpressionAnalysis>	find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByInvestigationIds(Collection<Long> investigationIds)
Collection<DifferentialExpressionAnalysis>	findByTaxon(Taxon taxon)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Collection<DifferentialExpressionAnalysis>	getAnalyses(BioAssaySet expressionExperiment)
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperiment(Collection<Long> ids)	Given a set of ids, find experiments or experimentsubsets that have differential expression analyses.
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperiment(Collection<Long> ids, int offset, int limit)
void	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
void	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)
void	update(DifferentialExpressionAnalysis o)
void	update(ExpressionAnalysisResultSet a)

Methods inherited from interface ubic.gemma.persistence.service.analysis.AnalysisService

findByInvestigation, findByInvestigations, findByName, findByUniqueInvestigations, getExperimentsWithAnalysis, getExperimentsWithAnalysis, load, loadAll, remove, removeForExperiment

Method Detail

countDownregulated

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countDownregulated(ExpressionAnalysisResultSet par,
                           double threshold)

Parameters:

par - result set

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

Returns:

number of downregulated elements

countProbesMeetingThreshold

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countProbesMeetingThreshold(ExpressionAnalysisResultSet ears,
                                    double threshold)

Parameters:

ears - result sets

threshold - (double) for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

Returns:

an integer count of all the probes that met the given threshold in the given expressionAnalysisResultSet

countUpregulated

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countUpregulated(ExpressionAnalysisResultSet par,
                         double threshold)

Parameters:

par - result set

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

create

@Secured("GROUP_USER")
DifferentialExpressionAnalysis create(DifferentialExpressionAnalysis analysis)

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> find(Gene gene,
                                                ExpressionAnalysisResultSet resultSet,
                                                double threshold)

findByFactor

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

findByInvestigationIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<Long,Collection<DifferentialExpressionAnalysis>> findByInvestigationIds(Collection<Long> investigationIds)

findByTaxon

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface AnalysisService<DifferentialExpressionAnalysis>

findExperimentsWithAnalyses

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

getAnalyses

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> getAnalyses(BioAssaySet expressionExperiment)

getAnalyses

Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

Parameters:

expressionExperiments - ees

Returns:

quite deeply thawed analyses (not the results themselves, but metadata)

thaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
void thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

thaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
void thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

thawFully

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(DifferentialExpressionAnalysis o)

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(ExpressionAnalysisResultSet a)

canDelete

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Parameters:

differentialExpressionAnalysis - analysis

Returns:

Is the analysis deleteable, or is it tied up with another entity that keeps it from being removed.

getAnalysesByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids)

Given a set of ids, find experiments or experimentsubsets that have differential expression analyses. Subsets are handled two ways: if the ID given is of a subset, or if the ID is of an experiment that has subsets. In the latter case, the return value will contain experiments that were not explicitly queried for.

Parameters:

ids - of experiments or experimentsubsets.

Returns:

map of bioassayset (valueobjects) to analyses (valueobjects) for each.

getAnalysesByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids,
                                                                                                                          int offset,
                                                                                                                          int limit)